JISC: GB/3D type fossils online

Friday, 8 January 2016

The GB/3D team are busy exploring various ways of financing
the next stage of the project – the inclusion of figured and cited specimens
and the British Geological Survey “Type & Stratigraphic Fossil Collection” –
a collection of a quarter of a million macrofossils that illustrates most of
the invertebrate and plant species and subspecies found in the UK, plus a good
selection of vertebrates. To build the case for funding, we need to document
the impact that the project is already having, and to do this, we need your
help.

Didymograptus murchisoni geminus (Hisinger)

If you have used any of the GB/3D resources, please consider
writing your project up as a guest blog for this site. It is a good opportunity to
include links to your own sites, plus any papers or articles you may have
written. If you would like to volunteer a guest blog, or simply offer an email
of support, please use the Email Dr Michael Howe facility on my BGS web page: http://www.bgs.ac.uk/staff/profiles/3858.html
. I look forward to hearing from you.

Wednesday, 23 December 2015

FIGURE 1. Historical photograph of the skeleton of the holotype
(BRSMG Cb 2335) of Atychodracon megacephalus (Stutchbury, 1846).
Photograph taken from glass plate negative in the Bristol City Museum & Art
Gallery, originally published by Swinton (1948). Bristol City Museum & Art
Gallery, reproduced with permission. Length of skeleton = 4960 mm

Plesiosaurs are an extinct group of
Mesozoic marine reptiles. Their fossil record ranges from the latest Triassic (approx. 200 million years ago) to the latest Cretaceous
(approx. 65 million years ago), and they have a short body with four flippers,
a long neck, and a head full of sharp teeth. They are unlike any modern day
animal and were once described as looking like a snake threaded through the
body of a turtle.

The five metre-long holotype specimen of ‘Plesiosaurus’megacephalus, from the Jurassic
of Street-on-the-Fosse, Somerset, was one of several plesiosaur specimens once displayed in the Bristol City
Museum and Art Gallery during the first half of the 20th Century. As
one of the earliest plesiosaurs to evolve
it is an important species for understanding the early history of the group.
Sadly, the fossil skeleton was destroyed along with many other specimens, when
the museum was struck by a bomb during the Second World War. This destroyed
fossil material is sometimes referred to as the ‘ghost collection’.

All was not lost, however. Moulds of
some of the fossils had been taken before the war. In the case of ‘Plesiosaurus’megacephalus, multiple casts of
its skull and forelimb were produced prior to its destruction, and these had
been deposited in the collections of several other museums (British Geological
Survey, Keyworth; Natural History Museum, London; Trinity College, Dublin).

These casts recently provided a valuable
resource for Dr Adam Smith, Curator of Natural Sciences and a palaeontologist
at the Nottingham Natural History Museum, Wollaton Hall. Smith used the
casts to conduct a research project on the ‘Plesiosaurus’megacephalus, published this
April in the open access journal Palaeontologia Electronica (18.1.20A
p.1-19). The study was facilitated by The Bristol Museum and Art Gallery, who
provided historical photographs of the ‘ghost collection’from their
archives. These show how the fossil skeletons appeared before they were
destroyed (Figure 1). To assist with the project, the British Geological
Survey produced three-dimensional digital laser scans of the casts as part
of their JISC-funded ‘GB3D fossil types
online’project. The
resulting virtual models can be rotated and studied on a computer screen, and
even printed with a 3D printer (Figure 2, 3).

The scientific study shows that ‘Plesiosaurus’ megacephalus is distinct from all other plesiosaurs, including Plesiosaurus, and so it is given a new name, Atychodracon, meaning ’Unfortunate Dragon’. This is in recognition of the unfortunate destruction of the original fossil, as well as the colloquial name ‘Sea Dragon’, sometimes applied to extinct swimming reptiles. The project also shows that fossil casts, and 3D laser scans, provide valuable data for palaeontologists - they can be described, measured, and coded into analyses. When the original fossil material has been lost, damaged or destroyed, the scientific value of casts increases even further. This study is the first publication to make use of the publicly available repository of 3D laser scans provided by the BGS. The Bristol Museum and Art Gallery is now investigating the possibility of using physical representations of their ‘ghost collection’ in future exhibitions, to bring long lost fossils such as Atychodracon ‘back to life’.

awarded to the GB/3D British Type Macrofossils online project, April 2015

As 2015 draws towards its close, it is a time for reflection
on progress and highlights for the year. Work continues on adding and updating
entries. We have, for example, a number of new images to add to existing
entries. We are also keen to discuss with the curators of collections not yet
included how we can add their material. Provided the data is in the correct
format, adding it is fairly simple and quick. We are also looking at ways to
finance extending the database to include figured and cited specimens and other
good representative material to make the database more comprehensive. Crowdfunding
is one method under consideration.

Graph showing monthly visits to the GB/3D website for the
last two years

One highlight has been the growth through the year in visits
to the GB/3D website. After a high of 72,000 visits during September 2013,
immediately after the launch, monthly visits declined to 2,500 a year ago – but
they have been rising steadily through 2015 and have now been over 4,000 for
several months. Such behaviour is well documented in project cycles – we have
been through the peak of “euphoria” and the trough of “despondency” and are hopefully entering a prolonged period of “optimism”.

Another highlight has been the coining of the first GB/3D DOIs for three casts of sections of 'Plesiosaurus' megacephalus in a recent Palaeontologica Electronica paper by Adam S. Smith - see http://palaeo-electronica.org/content/2015/1146-plesiosaurus-megacephalus . Adam has prepared a guest blog on the subject.

The main highlight of the year was the receipt of the
International Data Rescue Award in the Geosciences, presented at EGU in Vienna,
in April.

The award was created to improve the prospects for preservation and
access of research data, particularly of dark data, and to share the varied ways
that these data are being processed, stored, and used. Lack of access may be
due to the nature of the formatting (e.g., analogue data, magnetic tapes that
lack format description) or the nature of the data curation and/or organization
(e.g., no formal database repository, no backup), such that those data cannot
be shared. Consequently, the progress of research suffers unless extra steps
are taken to recover the data or transform them to a dependable electronic
media.

In our case, the award marked the provision of a single database to
locate type material in numerous museum collections, and to facilitate access
by providing high resolution images and stereo-anaglyphs, and in many cases, 3d
digital models.

Thursday, 30 April 2015

A selection of stereoscopic GB/3D Type Fossils project fossil images were displayed in a special exhibition organized during the 2 days’ annual school fair “Panigiri Scholis Moraiti” in Greece.

The fair was held on 4-5 April 2015 at the Moraitis’ School buildings in Psychiko, a suburb north of the Greek capital, Athens. The event is organized by its high-school students once a year and hosts activities and events in order to raise money for charity. The specific exhibition was prepared by the high school “Nature observation and interpretation Group”.

The aim of the exhibition was to portray the possible landscape, flora and fauna of the wider school area during different geological periods and to feature the importance of the fossils in understanding about how life evolved on earth.

Due to GB/3D Type Fossils project help, the visitors had the opportunity to examine typical fossils of animals that lived during the long distant past, using special red-cyan glasses prepared by the students. The project also inspired the students to make their own stereoscopic images using pairs of photographs and relevant free software.

In addition, representative digital models, scanned and provided online by the GB/3D Type Fossils project, were 3d printed in the main entrance hall in order to attract the visitors’ attention, and to promote the new technology potentials and the pioneer initiatives!

Friday, 27 February 2015

In a previous post, we talked about the value of geo-locating some
of the 20,000 or so fossil specimens we have processed in the 3D Fossils
database. In this post, I want to explain a little more why it is useful, and
also how we do it.

Visitors to the 3D Fossils site can at the moment choose to search
by a number of criteria, for example, if I search for fossils from the
Carboniferous I will return specimens around 300-360 million years old. However
if I search for “Lyme Regis” I will only get those specimens where the location
field contains at least those words. I won't see specimens from Charmouth, or
Pinhay, both only a couple of miles away. At the moment, our system is not
aware of any geospatial relations between the text in the locality field.

To fix this, we need to know where all our places are on the British
National Grid. In the modern world where even your mobile phone knows exactly
where it is within just a few metres, it is easy to forget that it was not
always this easy :

A lot
of our specimens were collected before the grid was standardised to the
OSGB 1936 format currently in place

Distances
were measured in miles or yards (sometimes even furlongs, rods and
chains), rather than metres and kilometres.

Many of
the localities are recorded in the style “small quarry (disused) on
south side of lane, around 250 yards east of Dog and Duck public house,
name of small village, etc”

There
are plenty of places in the UK which share the same name, but are in
completely different places. Examples might include Gillingham,
Kent/Gillingham, Dorset, or Rainham, Kent/Rainham, Essex.

If two
places sharing the same name is not confusing enough, some places like to
move around. Dudley, in the two hundred or so years since it was
recognised as a source of prime geological material, has been part of
Worcestershire, Staffordshire and the West Midlands.

Sometimes,
fossil dealers would not be keen to disclose the sources of their stock
for fear of losing out on a sale. Hence we often see wonderful fossils
with only scant location information, for example “Whitby” or “Lyme Regis”

•Finally, sometimes the locality information can be so precise that there might be a risk of exposing the exact location of sites that may be on private land. In this case we obfuscate the locality slightly, whilst retaining full details on file should they ever be required for bona fide research.

Despite these challenges, we can use our resources to make our best estimate of the right place on the map, and we are being helped by a number of volunteers who can carry out a few minutes of investigation work for each one. Some of the resources we like to use are:

•Ordnance Survey maps, old and new. We are lucky to have a comprehensive back catalogue of these, and in digital format too. We use GIS packages such as ArcGIS to examine them.

•Geological maps, usually based on an OS map underneath, but the geology listed in the specimen data might be a valuable extra clue. You can have a look at some of our maps using the new Maps Portal

•Gazeteers (such as the OS Open Data 50k version, or GeoNames, a crowdsourced alternative). These are simply lists of place names and their grid references. They can be very useful to simply get you to the right area to start looking, or where the locality information is so vague that there is no way to get any more accuracy.

•Web searches – sometimes old quarries will have become SSSI or RIGS sites and accompanying paperwork on these will often yield a grid reference. Similarly the original published descriptions of the specimens may provide location details

•Friends and colleagues – sometimes, if a description is particularly ambiguous, contains colloquial references, or is spelled incorrectly, no amount of web searching will help. However, someone who is familiar with the area might instantly say “I know exactly where that is”!

When we find a point that we believe represents as accurately as possible where the fossil was found, it is just a matter of reading off a 12 digit reference (which represents the position, in metres, east and north of a datum point off the Isles of Scilly). We are compiling all these points into a database, which we can use to quality check the final results. I'll explain how we do that in a future post.

We are a little more than half way through a list of around 4,000 points from the 3d Fossils database, but if you think this sounds like an interesting task then there are plenty more parts of our collection that would benefit from the same treatment. You can volunteer from home too, but if you're ever near Keyworth we'd be happy to show you around. Contact simhar@bgs.ac.uk in the first instance.

Tuesday, 17 February 2015

It may be 18 months since the end of official Jisc funding for the GB/3D Type
Fossils Online Project, but development of this important resource has continued apace. Some of our volunteers have been georeferencing (or
geolocating) many of the fossil localities. Georeferencing is the addition of a
grid reference, or latitude and longitude, to a location, and it will be
described in more detail in a forthcoming post. The aim of georeferencing is to
allow localities to be plotted more easily on a map, or in a GIS (Geographical
Information System), and then subjected to more rigorous
analysis. As a geological survey, our traditional business has always been the
production of geological maps, and not surprisingly, we are heavily involved in
GIS. We have an online GIS known as “GeoIndex”, which provides access to many
of our datasets and is available at: http://mapapps2.bgs.ac.uk/geoindex/home.html
.

The BGS has recently made over 6000 geological maps and
sections available through its online Maps Portal. The 1:50,000 (and previously
1:63,360) maps established a standard which many other geological surveys
around the world have endeavoured to copy. Typical map sheets now include not
only the basic map and key, but generally several cross-sections and a
“generalised vertical section”. Some maps also include geophysical, metamorphic
& biostratigraphic data, and a summary geological history.
Key “marginalia”
on the Sidmouth Sheet (below) include:

Two horizontal cross sections, showing the general relations
of the rocks along the two lines drawn on the map. The vertical scale is x2

Generalised vertical section. This acts as a key, drawn roughly
to scale, indicating thickness variations, and the relationships between the solid
geology lithostratigraphic units. Dominant lithologies are also described

The online maps portal is available at: http://www.bgs.ac.uk/data/maps/home.html
. It allows you to select from the latest versions of the 1:50,000 geological
maps, or many of the older versions, plus many other small scale maps and
sections. For each map or section there is a detailed record of the metadata
and links to view or buy the map. The link to view the map open a high
resolution JPEG2000 image within the IIPMooViewer (IIPImage HTML5 Ajax High
Resolution Image Viewer), which allows you to zoom in and move around the
screen. At full magnification (typically around x3), you can see more on the
image that you can on the original – at least without a magnifying glass.

The inclusion of all the historical maps allows the user to
appreciate the understanding of the geology and the stratigraphical nomenclature
that would have been current at any point in time, for example when a
particular fossil was collected. One of the key localities in the GB3D database
is Lyme Regis, and I have included extracts from the 2005 and 1846 maps. I will
leave the reader to compare the two.

Thursday, 10 April 2014

The GB3D Fossil Types Online stand in the Technology Garden at the Jisc Digital Festival 2014 in Birmingham raised significant interest in 3d-printing and the power of digital models for sharing objects and ideas.

If you don't have access to a 3d printer, you can still appreciate the fossil in three dimensions by viewing the 3d stereo anaglyphs - all you need is a pair of red-cyan glasses that you can buy online for around a pound...